Update to incorporate latest Development branch patches

lib/BasicTypes.h

@@ -104,44 +104,38 @@ inline void record_debug(uint *x, uint len, std::string filename,
 
 //******************************************************************************
 
-typedef unsigned int uint;
-typedef unsigned long int ulong;
-
-#define UNUSED(x) (void)(x)
-
-// single XYZ for use as a temporary and return type
-struct XYZ {
-  double x, y, z;
-
+// single XYZ coordinate for use as a temporary and return type
+class XYZ {
+public:
   XYZ() : x(0.0), y(0.0), z(0.0) {}
   XYZ(double xVal, double yVal, double zVal) : x(xVal), y(yVal), z(zVal) {}
+
+  friend inline std::ostream &operator<<(std::ostream &stream, const XYZ &p);
+
+  inline double getX() const { return x; }
+  inline double getY() const { return y; }
+  inline double getZ() const { return z; }
+
   void Reset() { x = y = z = 0.0; }
   XYZ &operator=(XYZ const &rhs) {
     x = rhs.x;
     y = rhs.y;
     z = rhs.z;
     return *this;
   }
-  bool operator==(XYZ const &rhs) {
-    if (x == rhs.x && y == rhs.y && z == rhs.z)
-      return true;
-    return false;
+  inline bool operator==(XYZ const &rhs) const {
+    return (x == rhs.x && y == rhs.y && z == rhs.z);
   }
-  bool operator!=(XYZ const &rhs) {
-    if (x != rhs.x || y != rhs.y || z != rhs.z)
-      return true;
-    return false;
+  inline bool operator!=(XYZ const &rhs) const {
+    return (x != rhs.x || y != rhs.y || z != rhs.z);
   }
-  bool operator<(XYZ const &rhs) {
-    if (x < rhs.x && y < rhs.y && z < rhs.z)
-      return true;
-    return false;
+  inline bool operator<(XYZ const &rhs) const {
+    return (x < rhs.x && y < rhs.y && z < rhs.z);
   }
-  bool operator>(XYZ const &rhs) {
-    if (x > rhs.x || y > rhs.y || z > rhs.z)
-      return true;
-    return false;
+  inline bool operator>(XYZ const &rhs) const {
+    return (x > rhs.x || y > rhs.y || z > rhs.z);
   }
+
   XYZ &operator+=(XYZ const &rhs) {
     x += rhs.x;
     y += rhs.y;
@@ -174,26 +168,26 @@ struct XYZ {
     return *this;
   }
 
-  XYZ operator+(XYZ const &rhs) const { return XYZ(*this) += rhs; }
-  XYZ operator-(XYZ const &rhs) const { return XYZ(*this) -= rhs; }
-  XYZ operator*(XYZ const &rhs) const { return XYZ(*this) *= rhs; }
-  XYZ operator/(XYZ const &rhs) const { return XYZ(*this) /= rhs; }
+  XYZ operator+(XYZ const &rhs) const { return XYZ(x+rhs.x, y+rhs.y, z+rhs.z); }
+  XYZ operator-(XYZ const &rhs) const { return XYZ(x-rhs.x, y-rhs.y, z-rhs.z); }
+  XYZ operator*(XYZ const &rhs) const { return XYZ(x*rhs.x, y*rhs.y, z*rhs.z); }
+  XYZ operator/(XYZ const &rhs) const { return XYZ(x/rhs.x, y/rhs.y, z/rhs.z); }
 
-  XYZ operator*(const double a) const { return XYZ(*this) *= a; }
+  XYZ operator*(const double a) const { return XYZ(x*a, y*a, z*a); }
 
-  XYZ operator-() const { return XYZ(*this) * -1.0; }
+  XYZ operator-() const { return XYZ(-x, -y, -z); }
 
   void Inverse() {
     x = 1.0 / x;
     y = 1.0 / y;
     z = 1.0 / z;
   }
 
-  double Length() const { return sqrt(LengthSq()); }
   double LengthSq() const { return x * x + y * y + z * z; }
+  double Length() const { return std::sqrt(LengthSq()); }
 
   XYZ &Normalize() {
-    *this *= (1 / Length());
+    *this *= (1.0 / Length());
     return *this;
   }
 
@@ -214,6 +208,9 @@ struct XYZ {
       m = z;
     return m;
   }
+
+public:
+  double x, y, z;
 };
 
 inline std::ostream &operator<<(std::ostream &stream, const XYZ &p) {

src/ConfigSetup.cpp

@@ -836,7 +836,7 @@ void ConfigSetup::Init(const char *fileName, MultiSim const *const &multisim) {
     } else if (CheckString(line[0], "IntraMEMC-1Freq")) {
       if (stringtod(line[1]) > 0.0) {
         sys.moves.intraMemc = stringtod(line[1]);
-        printf("%-40s %-4.4f \n", "Info: IntraMEMC-2 move frequency",
+        printf("%-40s %-4.4f \n", "Info: IntraMEMC-1 move frequency",
                sys.moves.intraMemc);
         sys.intraMemcVal.enable = true;
         sys.intraMemcVal.MEMC1 = true;

src/Main.cpp

@@ -111,13 +111,12 @@ int main(int argc, char *argv[]) {
 #if defined _OPENMP && _OPENMP < 201511
     printf("Warning: OpenMP version < 4.5. GOMC will not run optimally!\n");
 #endif
-    // Print OpenMP version if recognized or OpenMP date code if not recognized.
+    // Print the OpenMP version if recognized or instead the OpenMP date code.
 #ifdef _OPENMP
     std::unordered_map<int, std::string> omp_map{
-        {200505, "2.5"}, {200805, "3.0"}, {201107, "3.1"},
-        {201307, "4.0"}, {201511, "4.5"}, {201611, "5.0 Preview 1"},
-        {201811, "5.0"}, {202011, "5.1"}, {202111, "5.2"},
-        {202411, "6.0"}};
+        {200505, "2.5"}, {200805, "3.0"}, {201107, "3.1"}, {201307, "4.0"},
+        {201511, "4.5"}, {201611, "5.0 Preview 1"}, {201811, "5.0"},
+        {202011, "5.1"}, {202111, "5.2"}, {202411, "6.0"}};
     auto match = omp_map.find(_OPENMP);
     if (match == omp_map.end())
       printf("%-40s %u\n", "Info: Compiled with OpenMP Version", _OPENMP);

src/Simulation.cpp

@@ -75,6 +75,14 @@ Simulation::~Simulation() {
 void Simulation::RunSimulation(void) {
   GOMC_EVENT_START(1, GomcProfileEvent::MC_RUN);
   double startEnergy = system->potential.totalEnergy.total;
+  if (!std::isfinite(startEnergy)) {
+    std::cout
+        << "Initial system has non-finite energy. This is usually caused"
+           " by two or more atoms in the initial configuration having "
+           "identical coordinates. Please correct your input file and rerun.\n";
+
+    exit(EXIT_FAILURE);
+  }
   if (totalSteps == 0) {
     for (int i = 0; i < (int)frameSteps.size(); i++) {
       if (i == 0) {